Basal Rot of : Understanding Pathogenicity in f. sp. .

is a globally distributed soilborne fungal pathogen causing root rots, bulb rots, crown rots and vascular wilts on a range of horticultural plants. Pathogenic isolates are highly host specific and are classified as . is an important ornamental crop and both the quality and yield of flowers and bulbs can be severely affected by a basal rot caused by f. sp. (FON); 154 isolates were obtained from different locations and cultivars in the United Kingdom, representing a valuable resource. A subset of 30 isolates were all found to be pathogenic and were therefore identified as FON. Molecular characterisation of isolates through sequencing of three housekeeping genes, suggested a monophyletic origin with little divergence. PCR detection of 14 () genes, previously shown to be associated with pathogenicity in other f. spp., revealed different complements of , , , and within FON isolates which may suggest a race structure. gene sequences were unique to FON and was present in all isolates, allowing for molecular identification of FON for the first time. The genome of a highly pathogenic isolate was sequenced and lineage specific (LS) regions identified which harboured putative effectors including the genes. Real-time RT-PCR, showed that genes and selected putative effectors were expressed with many significantly upregulated during infection. This is the first study to characterise molecular variation in FON and provide an analysis of the FON genome. Identification of expressed genes potentially associated with virulence provides the basis for future functional studies and new targets for molecular diagnostics.